From f101cfe06d0966bcf6da6cfa4dd9f3b48ec6cb4f Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Thu, 6 Jun 2024 16:54:18 -0700
Subject: [PATCH 1/8] update pyproject.toml and workflows

---
 .github/workflows/build.yml | 31 ++++++++--------
 .github/workflows/test.yml  | 72 ++++++++++++++++++-------------------
 conda_recipe/meta.yaml      | 26 ++++++++------
 pyproject.toml              | 50 ++++++++++++++++++++++++--
 qss/__init__.py             |  1 +
 setup.py                    | 35 ------------------
 6 files changed, 115 insertions(+), 100 deletions(-)
 delete mode 100644 setup.py

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 5adb464..0404f92 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -12,20 +12,20 @@ jobs:
           
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
               python-version: "3.9"
 
-          - name: Install Twine
-            run: sudo pip install twine
+          - name: Install Twine and Build
+            run: sudo pip install twine build
 
           - name: Create the distribution
             run: |
               git fetch --prune --unshallow --tags
-              sudo python setup.py sdist bdist_wheel
+              sudo python3 -m build
 
           - name: Publish package distributions to PyPI
             uses: pypa/gh-action-pypi-publish@release/v1
@@ -39,10 +39,10 @@ jobs:
             shell: bash -l {0}
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
               python-version: "3.9"
 
@@ -53,13 +53,13 @@ jobs:
               activate-environment: ""
               miniconda-version: "latest"
 
-          - name: Install the Mamba Dependencies
-            run: | 
+          - name: Install the Conda Dependencies
+            run: |
               conda config --set always_yes yes --set auto_update_conda false
               conda update conda
-              conda install mamba -n base -c conda-forge
               conda install -n base conda-libmamba-solver
-              mamba install python=3.9 "conda-build=3.21" colorama pip ruamel ruamel.yaml rich mamba jsonschema -c conda-forge
+              conda install python=3.9 conda-build colorama pip ruamel ruamel.yaml rich jsonschema -c conda-forge
+              git fetch --prune --unshallow --tags
               pip install -e .
 
 # run install twice due to client-size to ensure all files downloaded
@@ -67,14 +67,13 @@ jobs:
 # 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: mambabuild
+            id: condabuild
             run: |
-              mamba install anaconda-client
+              conda install anaconda-client
               conda config --set anaconda_upload no --set solver libmamba
               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 conda-forge -c stanfordcvxgrp --numpy 1.16.4
-              echo '::set-output name=gitversion::$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)'
+              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-) conda build . -c anaconda -c conda-forge -c stanfordcvxgrp          
+              echo "gitversion=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)" >> $GITHUB_OUTPUT
 
           - name: Upload the Anaconda Package
             id: condaload
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 9efaa47..c4001ab 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,53 +1,53 @@
 name: Main Test
-on:
-    pull_request:
-    push:
-        branches:
-            - master
-        tags:
-          - '*'
+
+on: [push]
 jobs:
     run-tests:
         runs-on: ubuntu-latest
+        environment: test
+        strategy:
+          fail-fast: false
+          matrix:
+            python-version: [ "3.10", "3.11", "3.12" ]
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
-              python-version: '3.9'
+              python-version: ${{ matrix.python-version }}
 
-          - name: Install Dependencies
-            run: | 
-              sudo python -m pip install -r requirements.txt
-              python -m pip install pytest
-              python -m pip install -e .
+          - name: Install Python Dependencies
+            run: |
+              curl -LsSf https://astral.sh/uv/install.sh | sh
+              uv pip install --system --break-system-packages -r requirements.txt
+              uv pip install --system --break-system-packages pytest pytest-cov pytest-github-report pytest-github-actions-annotate-failures
 
-# Current unit test is not consistent. Occasionally fails despite usually passing. Needs to be fixed.
           - name: Run Unit Tests
-            run: |
-              python -m pytest --import-mode=append tests/
+            env:
+              pytest_github_report: true
+              pytest_verbosity: 2
+            run: pytest -v --cov=src --cov-report=xml --cov-report=term-missing --color=yes tests/
 
     test-build-pypi:
-        needs: run-tests
         runs-on: ubuntu-latest
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
               python-version: "3.9"
 
-          - name: Install Twine
-            run: sudo pip install twine
+          - name: Install Twine and Build
+            run: sudo pip install twine build
 
           - name: Create the distribution
             run: |
               git fetch --prune --unshallow --tags
-              sudo python setup.py sdist bdist_wheel
+              sudo python3 -m build
 
     test-build-conda:
         needs: run-tests
@@ -58,27 +58,27 @@ jobs:
             shell: bash -l {0}
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
               python-version: "3.9"
 
           - name: Install Miniconda
-            uses: conda-incubator/setup-miniconda@v2
+            uses: conda-incubator/setup-miniconda@v3
             with:
               auto-activate-base: true
               activate-environment: ""
               miniconda-version: "latest"
 
-          - name: Install the Mamba Dependencies
-            run: | 
+          - name: Install the Conda Dependencies
+            run: |
               conda config --set always_yes yes --set auto_update_conda false
               conda update conda
-              conda install mamba -n base -c conda-forge
               conda install -n base conda-libmamba-solver
-              mamba install python=3.9 "conda-build=3.21" colorama pip ruamel ruamel.yaml rich mamba jsonschema -c conda-forge
+              conda install python=3.9 conda-build colorama pip ruamel ruamel.yaml rich jsonschema -c conda-forge
+              git fetch --prune --unshallow --tags
               pip install -e .
 
 
@@ -87,10 +87,10 @@ jobs:
 # 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: mambabuild
+            id: condabuild
             run: |
-              mamba install anaconda-client
+              conda install anaconda-client
+              conda clean --all
               conda config --set anaconda_upload no --set solver libmamba
-              git fetch --prune --unshallow --tags
-              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-) conda build . -c conda-forge -c stanfordcvxgrp --numpy 1.16.4
-              echo '::set-output name=gitversion::$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)'
+              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)test conda build . -c conda-forge -c stanfordcvxgrp
+              echo "gitversion=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)" >> $GITHUB_OUTPUT
diff --git a/conda_recipe/meta.yaml b/conda_recipe/meta.yaml
index 7d567b6..a00361d 100644
--- a/conda_recipe/meta.yaml
+++ b/conda_recipe/meta.yaml
@@ -5,7 +5,7 @@ package:
   version: {{ environ.get('VERSION_FROM_GIT_TAG') }}
 
 source:
-  git_url: https://github.com/cvxgrp/qss
+  path: .. # checked out repo instead of main repo branch
 
 build:
   noarch: python
@@ -16,27 +16,30 @@ requirements:
   host:
     - pip
     - python >=3.6
-    - scipy
-    - numpy >=1.16
-    - qdldl-python
-    - cvxpy
-    - matplotlib
 
   run:
     - pip
     - python
     - scipy
-    - numpy >=1.16
+    - numpy
     - qdldl-python
     - cvxpy
     - matplotlib
 
+test:
+  imports:
+    - qss
+  commands:
+    - pip check
+  requires:
+    - pip
+
 about:
   home: https://github.com/cvxgrp/qss
-  license: BSD
-  license_family: BSD
-  license_file:
-  summary: QSS Quadratic-Seperable Solver
+  license: Apache
+  license_family: Apache
+  license_file: LICENSE
+  summary: QSS Quadratic-Separable Solver
   doc_url:
   dev_url:
 
@@ -44,3 +47,4 @@ extra:
   recipe-maintainers:
     - lukevolpatti
     - Thistleman
+    - pluflou
diff --git a/pyproject.toml b/pyproject.toml
index a7a6804..4e3abe9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,49 @@
 [build-system]
-requires      = ["setuptools>=61.0.0", "wheel"]
-build-backend = "setuptools.build_meta"
\ No newline at end of file
+requires = ["setuptools>=64.0", "setuptools-scm[toml]"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qss"
+description = "QSS: Quadratic-Separable Solver"
+readme = "README.md"
+license.file = "LICENSE"
+authors = [
+  { name = "Luke Volpatti", email = "bennetm@stanford.edu" },
+]
+maintainers = [
+  { name = "Sara Miskovich", email = "smiskov@slac.stanford.edu" },
+]
+requires-python = ">=3.6"
+
+dependencies = [
+    "scipy",
+    "numpy",
+    "cvxpy",
+    "qdldl",
+    "matplotlib"
+]
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+]
+dynamic = ["version"]
+[tool.setuptools_scm]
+write_to = "qss/_version.py"
+
+[tool.setuptools.packages.find]
+include = ["qss*"]
+
+[project.urls]
+Homepage = "https://github.com/cvxgrp/qss"
+"Bug Tracker" = "https://github.com/cvxgrp/qss/issues"
diff --git a/qss/__init__.py b/qss/__init__.py
index 5e8f89f..a1b8326 100644
--- a/qss/__init__.py
+++ b/qss/__init__.py
@@ -1 +1,2 @@
+from ._version import version as __version__
 from qss.qss import QSS
diff --git a/setup.py b/setup.py
deleted file mode 100644
index a768c04..0000000
--- a/setup.py
+++ /dev/null
@@ -1,35 +0,0 @@
-from setuptools import setup
-import subprocess
-
-with open("README.md", "r", encoding="utf-8") 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="qss",
-    version=VERSION_FROM_GIT_TAG,
-    author="Luke Volpatti",
-    description="QSS: Quadratic-Separable Solver",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    install_requires=["numpy", "scipy", "qdldl", "cvxpy"],
-    url="https://github.com/lukevolpatti/qss",
-    project_urls={
-        "Bug Tracker": "https://github.com/lukevolpatti/qss/issues",
-    },
-    license="Apache 2.0",
-    packages=["qss"],
-    python_requires=">=3.6",
-)

From 17206bef8753844ef2572ae0b886c7396a3a4d29 Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Thu, 6 Jun 2024 17:01:27 -0700
Subject: [PATCH 2/8] update workflow to run at PR

---
 .github/workflows/test.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c4001ab..42956e2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,6 +1,10 @@
 name: Main Test
 
-on: [push]
+on:
+  push:
+  pull_request:
+    branches: [main]
+    types: [opened, reopened]
 jobs:
     run-tests:
         runs-on: ubuntu-latest

From 5bbb48f095548f29b7b55bf197eb5f17af964e7a Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Thu, 6 Jun 2024 17:04:34 -0700
Subject: [PATCH 3/8] add version file to pass tests in ci/cd

---
 qss/_version.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 qss/_version.py

diff --git a/qss/_version.py b/qss/_version.py
new file mode 100644
index 0000000..6c13460
--- /dev/null
+++ b/qss/_version.py
@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.2.4.dev2+g17206be'
+__version_tuple__ = version_tuple = (0, 2, 4, 'dev2', 'g17206be')

From 42c44fda32c9c7400287f6d704b2c0becce75f85 Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Thu, 6 Jun 2024 17:15:09 -0700
Subject: [PATCH 4/8] rm condition on conda build test

---
 .github/workflows/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 42956e2..f9bcfb4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -54,7 +54,6 @@ jobs:
               sudo python3 -m build
 
     test-build-conda:
-        needs: run-tests
         runs-on: ubuntu-latest
 # sets default shell to remove need for source to run the conda shell
         defaults:

From 466448040c33f2496c67cef28c0bde15df3eddd7 Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Thu, 6 Jun 2024 17:22:34 -0700
Subject: [PATCH 5/8] add test trigger to PR edits

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f9bcfb4..e98edfe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -4,7 +4,7 @@ on:
   push:
   pull_request:
     branches: [main]
-    types: [opened, reopened]
+    types: [opened, edited, reopened]
 jobs:
     run-tests:
         runs-on: ubuntu-latest

From 802eb7243b88a2a8dc676962007f6283d5419ee3 Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Fri, 7 Jun 2024 11:26:38 -0700
Subject: [PATCH 6/8] Fix bug in conda build upload

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 0404f92..6cb9c22 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -78,4 +78,4 @@ jobs:
           - name: Upload the Anaconda Package
             id: condaload
             run: |
-              anaconda upload -u stanfordcvxgrp  /usr/share/miniconda3/conda-bld/noarch/qss-${{ steps.mambabuild.outputs.gitversion }}-*.tar.bz2
+              anaconda upload -u stanfordcvxgrp  /usr/share/miniconda3/conda-bld/noarch/qss-${{ steps.condabuild.outputs.gitversion }}-*.tar.bz2

From c910f3cc41ae1a55110f71970ef0c117e7800820 Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Wed, 4 Sep 2024 16:04:42 -0700
Subject: [PATCH 7/8] removes versioning (wip)

---
 pyproject.toml  |  1 -
 qss/__init__.py |  1 -
 qss/_version.py | 16 ----------------
 3 files changed, 18 deletions(-)
 delete mode 100644 qss/_version.py

diff --git a/pyproject.toml b/pyproject.toml
index 4e3abe9..a69b697 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,6 @@ classifiers = [
 ]
 dynamic = ["version"]
 [tool.setuptools_scm]
-write_to = "qss/_version.py"
 
 [tool.setuptools.packages.find]
 include = ["qss*"]
diff --git a/qss/__init__.py b/qss/__init__.py
index a1b8326..5e8f89f 100644
--- a/qss/__init__.py
+++ b/qss/__init__.py
@@ -1,2 +1 @@
-from ._version import version as __version__
 from qss.qss import QSS
diff --git a/qss/_version.py b/qss/_version.py
deleted file mode 100644
index 6c13460..0000000
--- a/qss/_version.py
+++ /dev/null
@@ -1,16 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple, Union
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-else:
-    VERSION_TUPLE = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-
-__version__ = version = '0.2.4.dev2+g17206be'
-__version_tuple__ = version_tuple = (0, 2, 4, 'dev2', 'g17206be')

From 44c0f4dd8aa38802d93af0aa71c0573ae942208d Mon Sep 17 00:00:00 2001
From: "Sara A. Miskovich" <saramiskovich@gmail.com>
Date: Mon, 16 Sep 2024 11:11:17 -0700
Subject: [PATCH 8/8] pins scipy until algo api changes fix

---
 conda_recipe/meta.yaml | 2 +-
 pyproject.toml         | 2 +-
 requirements.txt       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conda_recipe/meta.yaml b/conda_recipe/meta.yaml
index a00361d..db59174 100644
--- a/conda_recipe/meta.yaml
+++ b/conda_recipe/meta.yaml
@@ -20,7 +20,7 @@ requirements:
   run:
     - pip
     - python
-    - scipy
+    - scipy==1.13.1
     - numpy
     - qdldl-python
     - cvxpy
diff --git a/pyproject.toml b/pyproject.toml
index a69b697..56782ab 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ maintainers = [
 requires-python = ">=3.6"
 
 dependencies = [
-    "scipy",
+    "scipy==1.13.1",
     "numpy",
     "cvxpy",
     "qdldl",
diff --git a/requirements.txt b/requirements.txt
index 5eab1bc..543f3de 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 numpy
-scipy
+scipy==1.13.1
 qdldl
 cvxpy
 matplotlib